Multiple sequence alignment - TraesCS1A01G053000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G053000 chr1A 100.000 2747 0 0 1 2747 34892701 34889955 0.000000e+00 5073.0
1 TraesCS1A01G053000 chr1A 83.072 957 106 32 822 1747 34940391 34939460 0.000000e+00 819.0
2 TraesCS1A01G053000 chr1A 84.242 330 34 9 1993 2316 34875031 34874714 3.440000e-79 305.0
3 TraesCS1A01G053000 chr1A 100.000 50 0 0 629 678 34892024 34891975 2.910000e-15 93.5
4 TraesCS1A01G053000 chr1A 100.000 50 0 0 678 727 34892073 34892024 2.910000e-15 93.5
5 TraesCS1A01G053000 chr1B 96.749 1138 28 5 678 1813 55017476 55016346 0.000000e+00 1888.0
6 TraesCS1A01G053000 chr1B 96.646 1133 29 5 683 1813 54978940 54977815 0.000000e+00 1873.0
7 TraesCS1A01G053000 chr1B 88.908 1154 97 18 678 1810 55242298 55241155 0.000000e+00 1393.0
8 TraesCS1A01G053000 chr1B 88.735 1154 99 18 678 1810 55206510 55205367 0.000000e+00 1382.0
9 TraesCS1A01G053000 chr1B 95.232 755 32 3 1993 2745 55016356 55015604 0.000000e+00 1192.0
10 TraesCS1A01G053000 chr1B 95.232 755 31 4 1993 2745 54977825 54977074 0.000000e+00 1190.0
11 TraesCS1A01G053000 chr1B 84.342 843 110 12 921 1747 55428975 55428139 0.000000e+00 806.0
12 TraesCS1A01G053000 chr1B 92.647 544 34 5 1 542 55243212 55242673 0.000000e+00 778.0
13 TraesCS1A01G053000 chr1B 91.912 544 38 5 1 542 55207256 55206717 0.000000e+00 756.0
14 TraesCS1A01G053000 chr1B 94.792 192 8 2 1804 1995 32368290 32368101 5.750000e-77 298.0
15 TraesCS1A01G053000 chr1B 95.420 131 5 1 548 678 55206590 55206461 9.970000e-50 207.0
16 TraesCS1A01G053000 chr1B 94.030 134 7 1 546 678 55017560 55017427 4.640000e-48 202.0
17 TraesCS1A01G053000 chr1B 97.980 99 2 0 580 678 55242347 55242249 3.640000e-39 172.0
18 TraesCS1A01G053000 chr1B 86.567 134 9 7 546 678 54979021 54978896 3.690000e-29 139.0
19 TraesCS1A01G053000 chrUn 93.246 1140 51 12 678 1810 10695481 10696601 0.000000e+00 1655.0
20 TraesCS1A01G053000 chrUn 91.310 725 45 11 2030 2747 10698317 10699030 0.000000e+00 974.0
21 TraesCS1A01G053000 chrUn 83.226 1091 133 29 683 1747 10650675 10651741 0.000000e+00 955.0
22 TraesCS1A01G053000 chrUn 83.150 1092 134 27 683 1747 353497 354565 0.000000e+00 952.0
23 TraesCS1A01G053000 chrUn 83.841 953 102 32 822 1747 10643930 10644857 0.000000e+00 859.0
24 TraesCS1A01G053000 chrUn 94.683 489 21 5 57 542 10694817 10695303 0.000000e+00 754.0
25 TraesCS1A01G053000 chrUn 95.000 140 7 0 539 678 10695391 10695530 1.280000e-53 220.0
26 TraesCS1A01G053000 chrUn 93.478 46 2 1 1990 2034 10696595 10696640 1.770000e-07 67.6
27 TraesCS1A01G053000 chr2D 81.076 1004 144 34 772 1746 471063194 471064180 0.000000e+00 760.0
28 TraesCS1A01G053000 chr2B 80.765 993 158 20 772 1746 550396939 550397916 0.000000e+00 745.0
29 TraesCS1A01G053000 chr1D 90.164 305 27 3 2326 2630 104287325 104287024 7.130000e-106 394.0
30 TraesCS1A01G053000 chr1D 87.805 328 33 2 1993 2315 35905115 35904790 7.180000e-101 377.0
31 TraesCS1A01G053000 chr1D 84.639 332 35 11 1993 2316 35793482 35793159 1.590000e-82 316.0
32 TraesCS1A01G053000 chr3D 95.050 202 8 2 1806 2006 61601009 61601209 1.590000e-82 316.0
33 TraesCS1A01G053000 chr3D 94.388 196 9 2 1805 1999 345758039 345758233 1.600000e-77 300.0
34 TraesCS1A01G053000 chr4D 94.975 199 6 4 1798 1993 133609244 133609047 2.660000e-80 309.0
35 TraesCS1A01G053000 chr4D 93.367 196 11 2 1802 1996 118244779 118244973 3.460000e-74 289.0
36 TraesCS1A01G053000 chr7D 96.237 186 6 1 1811 1996 48555432 48555248 1.240000e-78 303.0
37 TraesCS1A01G053000 chr6D 95.288 191 7 2 1811 2001 2898973 2899161 4.450000e-78 302.0
38 TraesCS1A01G053000 chr6D 93.878 196 11 1 1811 2006 224491 224685 7.440000e-76 294.0
39 TraesCS1A01G053000 chr5D 96.216 185 6 1 1811 1995 526241577 526241394 4.450000e-78 302.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G053000 chr1A 34889955 34892701 2746 True 1753.333333 5073 100.000000 1 2747 3 chr1A.!!$R3 2746
1 TraesCS1A01G053000 chr1A 34939460 34940391 931 True 819.000000 819 83.072000 822 1747 1 chr1A.!!$R2 925
2 TraesCS1A01G053000 chr1B 55015604 55017560 1956 True 1094.000000 1888 95.337000 546 2745 3 chr1B.!!$R4 2199
3 TraesCS1A01G053000 chr1B 54977074 54979021 1947 True 1067.333333 1873 92.815000 546 2745 3 chr1B.!!$R3 2199
4 TraesCS1A01G053000 chr1B 55428139 55428975 836 True 806.000000 806 84.342000 921 1747 1 chr1B.!!$R2 826
5 TraesCS1A01G053000 chr1B 55205367 55207256 1889 True 781.666667 1382 92.022333 1 1810 3 chr1B.!!$R5 1809
6 TraesCS1A01G053000 chr1B 55241155 55243212 2057 True 781.000000 1393 93.178333 1 1810 3 chr1B.!!$R6 1809
7 TraesCS1A01G053000 chrUn 10650675 10651741 1066 False 955.000000 955 83.226000 683 1747 1 chrUn.!!$F3 1064
8 TraesCS1A01G053000 chrUn 353497 354565 1068 False 952.000000 952 83.150000 683 1747 1 chrUn.!!$F1 1064
9 TraesCS1A01G053000 chrUn 10643930 10644857 927 False 859.000000 859 83.841000 822 1747 1 chrUn.!!$F2 925
10 TraesCS1A01G053000 chrUn 10694817 10699030 4213 False 734.120000 1655 93.543400 57 2747 5 chrUn.!!$F4 2690
11 TraesCS1A01G053000 chr2D 471063194 471064180 986 False 760.000000 760 81.076000 772 1746 1 chr2D.!!$F1 974
12 TraesCS1A01G053000 chr2B 550396939 550397916 977 False 745.000000 745 80.765000 772 1746 1 chr2B.!!$F1 974

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
768 1068 0.396435 CTGCCACTACCAGGAACACA 59.604 55.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 4383 0.10412 GTTTTGCCCCAACGAAGCTT 59.896 50.0 0.0 0.0 0.0 3.74 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.785189 ATACCGGCGGCGATGACAC 62.785 63.158 34.49 0.00 0.00 3.67
108 110 1.758936 TCGAAGATCCCGCTCACTTA 58.241 50.000 0.71 0.00 0.00 2.24
115 117 2.088104 TCCCGCTCACTTATCTCCAT 57.912 50.000 0.00 0.00 0.00 3.41
132 134 2.050144 CCATGTAGAGGGCATGTAGGT 58.950 52.381 0.00 0.00 41.38 3.08
209 212 5.011023 AGGGTTTTAGCTTGATTGTTCCTTG 59.989 40.000 0.00 0.00 0.00 3.61
210 213 5.230182 GGTTTTAGCTTGATTGTTCCTTGG 58.770 41.667 0.00 0.00 0.00 3.61
238 241 6.744112 TCAATTAAGCCTTCGTGTGATTTTT 58.256 32.000 0.00 0.00 0.00 1.94
459 464 1.301244 CTGTCGTGGCTCTTGCAGT 60.301 57.895 0.00 0.00 41.91 4.40
496 501 4.632251 GGAATCGTAGCATAGAGAGATCGA 59.368 45.833 0.00 0.00 0.00 3.59
498 503 2.997303 TCGTAGCATAGAGAGATCGAGC 59.003 50.000 0.00 0.00 0.00 5.03
511 516 3.531538 AGATCGAGCCGAAGCATTTAAA 58.468 40.909 0.00 0.00 43.56 1.52
542 547 1.074951 GGCCTAGGTGTGCAGGTTT 59.925 57.895 11.31 0.00 34.18 3.27
543 548 0.539669 GGCCTAGGTGTGCAGGTTTT 60.540 55.000 11.31 0.00 34.18 2.43
544 549 1.328279 GCCTAGGTGTGCAGGTTTTT 58.672 50.000 11.31 0.00 34.18 1.94
545 550 1.269723 GCCTAGGTGTGCAGGTTTTTC 59.730 52.381 11.31 0.00 34.18 2.29
546 551 2.582052 CCTAGGTGTGCAGGTTTTTCA 58.418 47.619 0.00 0.00 0.00 2.69
568 693 1.533711 GGGCTGTATGCATGGGAGT 59.466 57.895 10.16 0.00 45.15 3.85
666 959 5.850557 AACATGACTTGTTCAAACCATGA 57.149 34.783 21.66 0.00 45.55 3.07
667 960 5.850557 ACATGACTTGTTCAAACCATGAA 57.149 34.783 21.66 0.00 45.71 2.57
768 1068 0.396435 CTGCCACTACCAGGAACACA 59.604 55.000 0.00 0.00 0.00 3.72
899 1222 1.699634 CTGGTCTCCTTCAACCCTTCA 59.300 52.381 0.00 0.00 34.47 3.02
935 1258 4.945246 TCACAACTCACAAGAACTAGTCC 58.055 43.478 0.00 0.00 0.00 3.85
952 1277 2.037251 AGTCCGCAGCTCTTTTGTCTAA 59.963 45.455 0.00 0.00 0.00 2.10
986 1312 5.163713 GGCACTTGATCTGGTGAGAATTAAC 60.164 44.000 18.09 3.02 35.69 2.01
1114 1441 1.352352 CTGACAGGACATCCCAAGGTT 59.648 52.381 0.00 0.00 37.41 3.50
1284 1662 5.476254 AGATTTCTTTTTCTCTGGCCTTCAG 59.524 40.000 3.32 0.00 44.68 3.02
1848 2226 3.132629 GCTATAGCGTCGCTAATAGCA 57.867 47.619 34.13 19.54 44.62 3.49
1849 2227 2.847133 GCTATAGCGTCGCTAATAGCAC 59.153 50.000 34.13 20.55 44.62 4.40
1850 2228 1.965083 ATAGCGTCGCTAATAGCACG 58.035 50.000 29.13 22.97 44.62 5.34
1851 2229 0.659427 TAGCGTCGCTAATAGCACGT 59.341 50.000 24.13 18.62 42.58 4.49
1852 2230 0.179145 AGCGTCGCTAATAGCACGTT 60.179 50.000 20.25 20.98 42.58 3.99
1853 2231 1.064505 AGCGTCGCTAATAGCACGTTA 59.935 47.619 20.25 2.88 42.58 3.18
1854 2232 2.049228 GCGTCGCTAATAGCACGTTAT 58.951 47.619 25.54 0.00 42.58 1.89
1855 2233 3.058708 AGCGTCGCTAATAGCACGTTATA 60.059 43.478 20.25 0.00 42.58 0.98
1856 2234 3.297461 GCGTCGCTAATAGCACGTTATAG 59.703 47.826 25.54 6.26 42.58 1.31
1857 2235 3.297461 CGTCGCTAATAGCACGTTATAGC 59.703 47.826 20.67 0.00 42.58 2.97
1858 2236 3.865428 CGCTAATAGCACGTTATAGCG 57.135 47.619 13.15 17.14 42.58 4.26
1859 2237 3.231965 CGCTAATAGCACGTTATAGCGT 58.768 45.455 20.20 8.97 42.58 5.07
1860 2238 4.397382 CGCTAATAGCACGTTATAGCGTA 58.603 43.478 14.48 0.00 42.58 4.42
1861 2239 5.026462 CGCTAATAGCACGTTATAGCGTAT 58.974 41.667 14.48 8.95 42.58 3.06
1862 2240 5.510674 CGCTAATAGCACGTTATAGCGTATT 59.489 40.000 14.48 12.77 42.58 1.89
1863 2241 6.504335 CGCTAATAGCACGTTATAGCGTATTG 60.504 42.308 14.48 4.15 42.58 1.90
1864 2242 6.525628 GCTAATAGCACGTTATAGCGTATTGA 59.474 38.462 14.48 1.49 43.83 2.57
1865 2243 6.929587 AATAGCACGTTATAGCGTATTGAG 57.070 37.500 14.48 3.36 43.83 3.02
1866 2244 4.563337 AGCACGTTATAGCGTATTGAGA 57.437 40.909 14.48 0.00 43.83 3.27
1867 2245 4.928601 AGCACGTTATAGCGTATTGAGAA 58.071 39.130 14.48 0.00 43.83 2.87
1868 2246 5.529791 AGCACGTTATAGCGTATTGAGAAT 58.470 37.500 14.48 0.00 43.83 2.40
1869 2247 5.983720 AGCACGTTATAGCGTATTGAGAATT 59.016 36.000 14.48 0.00 43.83 2.17
1870 2248 6.065153 GCACGTTATAGCGTATTGAGAATTG 58.935 40.000 14.48 0.00 43.83 2.32
1871 2249 6.065153 CACGTTATAGCGTATTGAGAATTGC 58.935 40.000 14.48 0.00 43.83 3.56
1872 2250 5.176958 ACGTTATAGCGTATTGAGAATTGCC 59.823 40.000 13.27 0.00 43.83 4.52
1873 2251 5.405571 CGTTATAGCGTATTGAGAATTGCCT 59.594 40.000 0.19 0.00 0.00 4.75
1874 2252 6.400091 CGTTATAGCGTATTGAGAATTGCCTC 60.400 42.308 0.19 0.00 0.00 4.70
1875 2253 2.205074 AGCGTATTGAGAATTGCCTCG 58.795 47.619 0.00 0.00 35.99 4.63
1876 2254 1.933853 GCGTATTGAGAATTGCCTCGT 59.066 47.619 0.00 0.00 35.99 4.18
1877 2255 2.351726 GCGTATTGAGAATTGCCTCGTT 59.648 45.455 0.00 0.00 35.99 3.85
1878 2256 3.554324 GCGTATTGAGAATTGCCTCGTTA 59.446 43.478 0.00 0.00 35.99 3.18
1879 2257 4.033587 GCGTATTGAGAATTGCCTCGTTAA 59.966 41.667 0.00 0.00 35.99 2.01
1880 2258 5.446741 GCGTATTGAGAATTGCCTCGTTAAA 60.447 40.000 0.00 0.00 35.99 1.52
1881 2259 6.715464 CGTATTGAGAATTGCCTCGTTAAAT 58.285 36.000 0.00 0.00 35.99 1.40
1882 2260 7.517734 GCGTATTGAGAATTGCCTCGTTAAATA 60.518 37.037 0.00 0.00 35.99 1.40
1883 2261 8.495949 CGTATTGAGAATTGCCTCGTTAAATAT 58.504 33.333 0.00 0.00 35.99 1.28
1887 2265 8.239681 TGAGAATTGCCTCGTTAAATATATCG 57.760 34.615 0.00 0.00 35.99 2.92
1888 2266 7.330946 TGAGAATTGCCTCGTTAAATATATCGG 59.669 37.037 0.00 0.00 35.99 4.18
1889 2267 7.159372 AGAATTGCCTCGTTAAATATATCGGT 58.841 34.615 0.00 0.00 0.00 4.69
1890 2268 6.721571 ATTGCCTCGTTAAATATATCGGTG 57.278 37.500 0.00 0.00 0.00 4.94
1891 2269 5.204409 TGCCTCGTTAAATATATCGGTGT 57.796 39.130 0.00 0.00 0.00 4.16
1892 2270 6.330004 TGCCTCGTTAAATATATCGGTGTA 57.670 37.500 0.00 0.00 0.00 2.90
1893 2271 6.151691 TGCCTCGTTAAATATATCGGTGTAC 58.848 40.000 0.00 0.00 0.00 2.90
1894 2272 6.151691 GCCTCGTTAAATATATCGGTGTACA 58.848 40.000 0.00 0.00 0.00 2.90
1895 2273 6.642131 GCCTCGTTAAATATATCGGTGTACAA 59.358 38.462 0.00 0.00 0.00 2.41
1896 2274 7.330208 GCCTCGTTAAATATATCGGTGTACAAT 59.670 37.037 0.00 0.00 0.00 2.71
1897 2275 8.644619 CCTCGTTAAATATATCGGTGTACAATG 58.355 37.037 0.00 0.00 0.00 2.82
1898 2276 9.188588 CTCGTTAAATATATCGGTGTACAATGT 57.811 33.333 0.00 0.00 0.00 2.71
1899 2277 9.184062 TCGTTAAATATATCGGTGTACAATGTC 57.816 33.333 0.00 0.00 0.00 3.06
1900 2278 9.188588 CGTTAAATATATCGGTGTACAATGTCT 57.811 33.333 0.00 0.00 0.00 3.41
1902 2280 7.869016 AAATATATCGGTGTACAATGTCTCG 57.131 36.000 0.00 0.00 0.00 4.04
1903 2281 1.922570 ATCGGTGTACAATGTCTCGC 58.077 50.000 0.00 0.00 0.00 5.03
1904 2282 0.885879 TCGGTGTACAATGTCTCGCT 59.114 50.000 0.00 0.00 0.00 4.93
1905 2283 2.086094 TCGGTGTACAATGTCTCGCTA 58.914 47.619 0.00 0.00 0.00 4.26
1906 2284 2.488937 TCGGTGTACAATGTCTCGCTAA 59.511 45.455 0.00 0.00 0.00 3.09
1907 2285 3.129813 TCGGTGTACAATGTCTCGCTAAT 59.870 43.478 0.00 0.00 0.00 1.73
1908 2286 4.336153 TCGGTGTACAATGTCTCGCTAATA 59.664 41.667 0.00 0.00 0.00 0.98
1909 2287 4.675565 CGGTGTACAATGTCTCGCTAATAG 59.324 45.833 0.00 0.00 0.00 1.73
1910 2288 4.444720 GGTGTACAATGTCTCGCTAATAGC 59.555 45.833 1.41 1.41 38.02 2.97
1911 2289 5.041287 GTGTACAATGTCTCGCTAATAGCA 58.959 41.667 13.15 0.00 42.58 3.49
1912 2290 5.041287 TGTACAATGTCTCGCTAATAGCAC 58.959 41.667 13.15 3.79 42.58 4.40
1913 2291 3.116300 ACAATGTCTCGCTAATAGCACG 58.884 45.455 13.15 2.42 42.58 5.34
1914 2292 1.772182 ATGTCTCGCTAATAGCACGC 58.228 50.000 13.15 0.19 42.58 5.34
1915 2293 0.738975 TGTCTCGCTAATAGCACGCT 59.261 50.000 13.15 0.00 42.58 5.07
1916 2294 1.944709 TGTCTCGCTAATAGCACGCTA 59.055 47.619 13.15 0.39 42.58 4.26
1917 2295 2.552743 TGTCTCGCTAATAGCACGCTAT 59.447 45.455 13.15 5.72 42.58 2.97
1918 2296 3.749609 TGTCTCGCTAATAGCACGCTATA 59.250 43.478 13.15 1.16 42.58 1.31
1919 2297 4.142881 TGTCTCGCTAATAGCACGCTATAG 60.143 45.833 13.15 10.32 42.58 1.31
1920 2298 3.102276 CTCGCTAATAGCACGCTATAGC 58.898 50.000 15.09 15.09 42.58 2.97
1946 2324 8.581057 GTGATATAGCACGCTAATAGCATATT 57.419 34.615 13.15 0.00 42.58 1.28
1947 2325 9.035607 GTGATATAGCACGCTAATAGCATATTT 57.964 33.333 13.15 0.91 42.58 1.40
1948 2326 9.599866 TGATATAGCACGCTAATAGCATATTTT 57.400 29.630 13.15 0.00 42.58 1.82
1949 2327 9.855361 GATATAGCACGCTAATAGCATATTTTG 57.145 33.333 13.15 0.00 42.58 2.44
1950 2328 7.905604 ATAGCACGCTAATAGCATATTTTGA 57.094 32.000 13.15 0.00 42.58 2.69
1951 2329 6.233430 AGCACGCTAATAGCATATTTTGAG 57.767 37.500 13.15 0.00 42.58 3.02
1952 2330 5.180117 AGCACGCTAATAGCATATTTTGAGG 59.820 40.000 13.15 0.00 42.58 3.86
1953 2331 5.049405 GCACGCTAATAGCATATTTTGAGGT 60.049 40.000 13.15 0.00 42.58 3.85
1954 2332 6.593978 CACGCTAATAGCATATTTTGAGGTC 58.406 40.000 13.15 0.00 42.58 3.85
1955 2333 5.405571 ACGCTAATAGCATATTTTGAGGTCG 59.594 40.000 13.15 0.00 42.58 4.79
1956 2334 5.163953 CGCTAATAGCATATTTTGAGGTCGG 60.164 44.000 13.15 0.00 42.58 4.79
1957 2335 5.390991 GCTAATAGCATATTTTGAGGTCGGC 60.391 44.000 7.49 0.00 41.89 5.54
1958 2336 1.299541 AGCATATTTTGAGGTCGGCG 58.700 50.000 0.00 0.00 0.00 6.46
1959 2337 0.317020 GCATATTTTGAGGTCGGCGC 60.317 55.000 0.00 0.00 0.00 6.53
1960 2338 1.299541 CATATTTTGAGGTCGGCGCT 58.700 50.000 7.64 0.00 0.00 5.92
1961 2339 2.479837 CATATTTTGAGGTCGGCGCTA 58.520 47.619 7.64 0.00 0.00 4.26
1962 2340 2.902705 TATTTTGAGGTCGGCGCTAT 57.097 45.000 7.64 0.00 0.00 2.97
1963 2341 2.038387 ATTTTGAGGTCGGCGCTATT 57.962 45.000 7.64 0.00 0.00 1.73
1964 2342 1.816074 TTTTGAGGTCGGCGCTATTT 58.184 45.000 7.64 0.00 0.00 1.40
1965 2343 1.816074 TTTGAGGTCGGCGCTATTTT 58.184 45.000 7.64 0.00 0.00 1.82
1966 2344 1.083489 TTGAGGTCGGCGCTATTTTG 58.917 50.000 7.64 0.00 0.00 2.44
1967 2345 1.352056 GAGGTCGGCGCTATTTTGC 59.648 57.895 7.64 0.00 0.00 3.68
1968 2346 1.078426 AGGTCGGCGCTATTTTGCT 60.078 52.632 7.64 0.00 0.00 3.91
1969 2347 1.062525 GGTCGGCGCTATTTTGCTG 59.937 57.895 7.64 0.00 38.85 4.41
1970 2348 1.644786 GGTCGGCGCTATTTTGCTGT 61.645 55.000 7.64 0.00 38.61 4.40
1971 2349 1.003851 GTCGGCGCTATTTTGCTGTA 58.996 50.000 7.64 0.00 38.61 2.74
1972 2350 1.004927 GTCGGCGCTATTTTGCTGTAG 60.005 52.381 7.64 0.00 38.61 2.74
1973 2351 0.316196 CGGCGCTATTTTGCTGTAGC 60.316 55.000 7.64 0.00 39.86 3.58
1977 2355 1.815132 GCTATTTTGCTGTAGCGTGC 58.185 50.000 0.00 0.00 45.83 5.34
1978 2356 1.398390 GCTATTTTGCTGTAGCGTGCT 59.602 47.619 0.00 0.00 45.83 4.40
1979 2357 2.607635 GCTATTTTGCTGTAGCGTGCTA 59.392 45.455 0.00 0.00 45.83 3.49
1980 2358 3.248602 GCTATTTTGCTGTAGCGTGCTAT 59.751 43.478 4.68 0.00 45.83 2.97
1981 2359 4.260784 GCTATTTTGCTGTAGCGTGCTATT 60.261 41.667 4.68 0.00 45.83 1.73
1982 2360 4.701956 ATTTTGCTGTAGCGTGCTATTT 57.298 36.364 4.68 0.00 45.83 1.40
1983 2361 4.497473 TTTTGCTGTAGCGTGCTATTTT 57.503 36.364 4.68 0.00 45.83 1.82
1984 2362 4.497473 TTTGCTGTAGCGTGCTATTTTT 57.503 36.364 4.68 0.00 45.83 1.94
2050 4109 2.566833 ATGGCTATGCTAATTCGGCA 57.433 45.000 8.18 8.18 44.05 5.69
2131 4190 2.835764 TCCGGTAGCAAAGGTGAACTAT 59.164 45.455 0.00 0.00 0.00 2.12
2132 4191 4.025360 TCCGGTAGCAAAGGTGAACTATA 58.975 43.478 0.00 0.00 0.00 1.31
2197 4256 8.462016 GTTTCATTATAGTTGCATGTTTCCTCT 58.538 33.333 0.00 0.00 0.00 3.69
2340 4399 2.258013 CGAAGCTTCGTTGGGGCAA 61.258 57.895 34.97 0.00 45.09 4.52
2348 4407 0.395862 TCGTTGGGGCAAAACTTGGA 60.396 50.000 0.00 0.00 0.00 3.53
2465 4528 4.020617 TCCAAGCCAGTCGCAGGG 62.021 66.667 0.00 0.00 41.38 4.45
2617 4681 1.946768 TGCCCAGTTTTGTCTTCGAAG 59.053 47.619 19.35 19.35 0.00 3.79
2652 4716 2.158534 TGCCTAGTGTTCACCATGGTTT 60.159 45.455 16.84 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.651503 ACCCCATGTCTATCACTAAGACTG 59.348 45.833 4.99 1.72 43.13 3.51
15 16 3.905968 TCGACCCCATGTCTATCACTAA 58.094 45.455 0.00 0.00 42.13 2.24
43 44 2.125147 ATGTGGGTGTCATCGCCG 60.125 61.111 0.00 0.00 44.47 6.46
54 55 2.173519 AGGAAAAGTGATGCATGTGGG 58.826 47.619 2.46 0.00 0.00 4.61
89 91 1.758936 TAAGTGAGCGGGATCTTCGA 58.241 50.000 11.91 0.00 0.00 3.71
115 117 1.273609 ACCACCTACATGCCCTCTACA 60.274 52.381 0.00 0.00 0.00 2.74
132 134 4.840680 CCTGATATATCTTGACCTCCACCA 59.159 45.833 13.79 0.00 0.00 4.17
209 212 5.353123 TCACACGAAGGCTTAATTGATTACC 59.647 40.000 0.00 0.00 0.00 2.85
210 213 6.417191 TCACACGAAGGCTTAATTGATTAC 57.583 37.500 0.00 0.00 0.00 1.89
439 444 3.426568 GCAAGAGCCACGACAGCC 61.427 66.667 0.00 0.00 33.58 4.85
459 464 6.321435 TGCTACGATTCCTTCTGATTCTCTTA 59.679 38.462 0.00 0.00 0.00 2.10
496 501 5.594317 AGTCCATATTTTAAATGCTTCGGCT 59.406 36.000 0.00 0.00 42.37 5.52
498 503 6.795399 ACAGTCCATATTTTAAATGCTTCGG 58.205 36.000 0.00 0.00 0.00 4.30
511 516 3.904339 CACCTAGGCCTACAGTCCATATT 59.096 47.826 8.91 0.00 0.00 1.28
568 693 6.320434 TCAAACATATTGTCATGGGGAGTA 57.680 37.500 0.00 0.00 0.00 2.59
660 953 9.363401 TGTACTAGCTAGTTGTATATTCATGGT 57.637 33.333 30.40 4.15 37.73 3.55
670 963 9.234827 TGTTCATACTTGTACTAGCTAGTTGTA 57.765 33.333 30.40 24.15 37.73 2.41
671 964 8.118976 TGTTCATACTTGTACTAGCTAGTTGT 57.881 34.615 30.40 23.05 37.73 3.32
672 965 9.025020 CATGTTCATACTTGTACTAGCTAGTTG 57.975 37.037 30.40 19.97 37.73 3.16
673 966 8.967918 TCATGTTCATACTTGTACTAGCTAGTT 58.032 33.333 30.40 15.22 37.73 2.24
674 967 8.407064 GTCATGTTCATACTTGTACTAGCTAGT 58.593 37.037 28.50 28.50 40.24 2.57
675 968 8.625651 AGTCATGTTCATACTTGTACTAGCTAG 58.374 37.037 19.44 19.44 32.73 3.42
676 969 8.521170 AGTCATGTTCATACTTGTACTAGCTA 57.479 34.615 4.10 0.00 32.73 3.32
677 970 7.411486 AGTCATGTTCATACTTGTACTAGCT 57.589 36.000 4.10 0.00 32.73 3.32
678 971 7.899974 CAAGTCATGTTCATACTTGTACTAGC 58.100 38.462 13.44 0.00 43.20 3.42
899 1222 4.398988 TGAGTTGTGAACTTGTGATGCTTT 59.601 37.500 0.00 0.00 43.03 3.51
935 1258 2.923655 TCGATTAGACAAAAGAGCTGCG 59.076 45.455 0.00 0.00 0.00 5.18
952 1277 2.027745 AGATCAAGTGCCTTGTGTCGAT 60.028 45.455 12.71 1.86 41.66 3.59
959 1285 2.082231 CTCACCAGATCAAGTGCCTTG 58.918 52.381 9.62 8.22 42.25 3.61
986 1312 1.226660 GCCATTTGGATGCGAACGG 60.227 57.895 0.00 0.00 37.39 4.44
1284 1662 2.109126 GCTCGTGTTCCCAGCCATC 61.109 63.158 0.00 0.00 0.00 3.51
1828 2206 2.847133 GTGCTATTAGCGACGCTATAGC 59.153 50.000 34.54 34.54 46.26 2.97
1829 2207 3.092135 CGTGCTATTAGCGACGCTATAG 58.908 50.000 28.67 26.76 46.26 1.31
1830 2208 2.481568 ACGTGCTATTAGCGACGCTATA 59.518 45.455 28.67 19.32 46.26 1.31
1831 2209 1.266175 ACGTGCTATTAGCGACGCTAT 59.734 47.619 28.67 19.98 46.26 2.97
1832 2210 0.659427 ACGTGCTATTAGCGACGCTA 59.341 50.000 25.04 25.04 46.26 4.26
1833 2211 0.179145 AACGTGCTATTAGCGACGCT 60.179 50.000 27.45 27.45 46.26 5.07
1834 2212 1.469917 TAACGTGCTATTAGCGACGC 58.530 50.000 26.15 13.03 46.26 5.19
1835 2213 3.297461 GCTATAACGTGCTATTAGCGACG 59.703 47.826 25.32 25.32 46.26 5.12
1836 2214 4.802664 GCTATAACGTGCTATTAGCGAC 57.197 45.455 10.94 9.06 46.26 5.19
1838 2216 3.865428 CGCTATAACGTGCTATTAGCG 57.135 47.619 17.36 17.36 46.26 4.26
1848 2226 8.679767 GAGGCAATTCTCAATACGCTATAACGT 61.680 40.741 6.41 6.41 40.35 3.99
1849 2227 5.405571 AGGCAATTCTCAATACGCTATAACG 59.594 40.000 0.00 0.00 39.50 3.18
1850 2228 6.400091 CGAGGCAATTCTCAATACGCTATAAC 60.400 42.308 0.00 0.00 33.59 1.89
1851 2229 5.633601 CGAGGCAATTCTCAATACGCTATAA 59.366 40.000 0.00 0.00 33.59 0.98
1852 2230 5.161358 CGAGGCAATTCTCAATACGCTATA 58.839 41.667 0.00 0.00 33.59 1.31
1853 2231 3.990469 CGAGGCAATTCTCAATACGCTAT 59.010 43.478 0.00 0.00 33.59 2.97
1854 2232 3.181479 ACGAGGCAATTCTCAATACGCTA 60.181 43.478 0.00 0.00 33.59 4.26
1855 2233 2.205074 CGAGGCAATTCTCAATACGCT 58.795 47.619 0.00 0.00 33.59 5.07
1856 2234 1.933853 ACGAGGCAATTCTCAATACGC 59.066 47.619 0.00 0.00 33.59 4.42
1857 2235 5.712217 TTAACGAGGCAATTCTCAATACG 57.288 39.130 0.00 0.00 33.59 3.06
1861 2239 8.708742 CGATATATTTAACGAGGCAATTCTCAA 58.291 33.333 0.00 0.00 33.59 3.02
1862 2240 7.330946 CCGATATATTTAACGAGGCAATTCTCA 59.669 37.037 0.00 0.00 33.59 3.27
1863 2241 7.331193 ACCGATATATTTAACGAGGCAATTCTC 59.669 37.037 0.00 0.00 0.00 2.87
1864 2242 7.117812 CACCGATATATTTAACGAGGCAATTCT 59.882 37.037 0.00 0.00 0.00 2.40
1865 2243 7.095355 ACACCGATATATTTAACGAGGCAATTC 60.095 37.037 0.00 0.00 0.00 2.17
1866 2244 6.708949 ACACCGATATATTTAACGAGGCAATT 59.291 34.615 0.00 0.00 0.00 2.32
1867 2245 6.228258 ACACCGATATATTTAACGAGGCAAT 58.772 36.000 0.00 0.00 0.00 3.56
1868 2246 5.603596 ACACCGATATATTTAACGAGGCAA 58.396 37.500 0.00 0.00 0.00 4.52
1869 2247 5.204409 ACACCGATATATTTAACGAGGCA 57.796 39.130 0.00 0.00 0.00 4.75
1870 2248 6.151691 TGTACACCGATATATTTAACGAGGC 58.848 40.000 0.00 0.00 0.00 4.70
1871 2249 8.644619 CATTGTACACCGATATATTTAACGAGG 58.355 37.037 0.00 0.00 0.00 4.63
1872 2250 9.188588 ACATTGTACACCGATATATTTAACGAG 57.811 33.333 0.00 0.00 0.00 4.18
1873 2251 9.184062 GACATTGTACACCGATATATTTAACGA 57.816 33.333 0.00 0.00 0.00 3.85
1874 2252 9.188588 AGACATTGTACACCGATATATTTAACG 57.811 33.333 0.00 0.00 0.00 3.18
1876 2254 9.401873 CGAGACATTGTACACCGATATATTTAA 57.598 33.333 0.00 0.00 0.00 1.52
1877 2255 7.539710 GCGAGACATTGTACACCGATATATTTA 59.460 37.037 0.00 0.00 0.00 1.40
1878 2256 6.365247 GCGAGACATTGTACACCGATATATTT 59.635 38.462 0.00 0.00 0.00 1.40
1879 2257 5.862323 GCGAGACATTGTACACCGATATATT 59.138 40.000 0.00 0.00 0.00 1.28
1880 2258 5.183331 AGCGAGACATTGTACACCGATATAT 59.817 40.000 0.00 0.00 0.00 0.86
1881 2259 4.517832 AGCGAGACATTGTACACCGATATA 59.482 41.667 0.00 0.00 0.00 0.86
1882 2260 3.318275 AGCGAGACATTGTACACCGATAT 59.682 43.478 0.00 0.00 0.00 1.63
1883 2261 2.686405 AGCGAGACATTGTACACCGATA 59.314 45.455 0.00 0.00 0.00 2.92
1884 2262 1.476891 AGCGAGACATTGTACACCGAT 59.523 47.619 0.00 0.00 0.00 4.18
1885 2263 0.885879 AGCGAGACATTGTACACCGA 59.114 50.000 0.00 0.00 0.00 4.69
1886 2264 2.554806 TAGCGAGACATTGTACACCG 57.445 50.000 0.00 0.00 0.00 4.94
1887 2265 4.444720 GCTATTAGCGAGACATTGTACACC 59.555 45.833 0.00 0.00 0.00 4.16
1888 2266 5.041287 TGCTATTAGCGAGACATTGTACAC 58.959 41.667 10.94 0.00 46.26 2.90
1889 2267 5.041287 GTGCTATTAGCGAGACATTGTACA 58.959 41.667 10.94 0.00 46.26 2.90
1890 2268 4.146616 CGTGCTATTAGCGAGACATTGTAC 59.853 45.833 10.94 0.00 46.26 2.90
1891 2269 4.287720 CGTGCTATTAGCGAGACATTGTA 58.712 43.478 10.94 0.00 46.26 2.41
1892 2270 3.116300 CGTGCTATTAGCGAGACATTGT 58.884 45.455 10.94 0.00 46.26 2.71
1893 2271 2.097202 GCGTGCTATTAGCGAGACATTG 60.097 50.000 10.94 0.00 46.26 2.82
1894 2272 2.128035 GCGTGCTATTAGCGAGACATT 58.872 47.619 10.94 0.00 46.26 2.71
1895 2273 1.338337 AGCGTGCTATTAGCGAGACAT 59.662 47.619 10.94 0.00 46.26 3.06
1896 2274 0.738975 AGCGTGCTATTAGCGAGACA 59.261 50.000 10.94 0.00 46.26 3.41
1897 2275 2.682952 TAGCGTGCTATTAGCGAGAC 57.317 50.000 10.94 3.28 46.26 3.36
1898 2276 3.181509 GCTATAGCGTGCTATTAGCGAGA 60.182 47.826 18.62 0.00 46.26 4.04
1899 2277 3.102276 GCTATAGCGTGCTATTAGCGAG 58.898 50.000 18.62 11.00 46.26 5.03
1900 2278 3.132629 GCTATAGCGTGCTATTAGCGA 57.867 47.619 18.62 0.92 46.26 4.93
1921 2299 8.581057 AATATGCTATTAGCGTGCTATATCAC 57.419 34.615 18.61 0.00 46.26 3.06
1922 2300 9.599866 AAAATATGCTATTAGCGTGCTATATCA 57.400 29.630 18.61 0.00 46.26 2.15
1923 2301 9.855361 CAAAATATGCTATTAGCGTGCTATATC 57.145 33.333 18.61 0.00 46.26 1.63
1924 2302 9.599866 TCAAAATATGCTATTAGCGTGCTATAT 57.400 29.630 18.61 9.39 46.26 0.86
1925 2303 8.996024 TCAAAATATGCTATTAGCGTGCTATA 57.004 30.769 18.61 7.66 46.26 1.31
1926 2304 7.065085 CCTCAAAATATGCTATTAGCGTGCTAT 59.935 37.037 18.61 5.81 46.26 2.97
1927 2305 6.368791 CCTCAAAATATGCTATTAGCGTGCTA 59.631 38.462 18.61 0.00 46.26 3.49
1928 2306 5.180117 CCTCAAAATATGCTATTAGCGTGCT 59.820 40.000 18.61 0.00 46.26 4.40
1929 2307 5.049405 ACCTCAAAATATGCTATTAGCGTGC 60.049 40.000 18.61 0.00 46.26 5.34
1930 2308 6.545504 ACCTCAAAATATGCTATTAGCGTG 57.454 37.500 18.61 3.72 46.26 5.34
1931 2309 5.405571 CGACCTCAAAATATGCTATTAGCGT 59.594 40.000 14.53 14.53 46.26 5.07
1932 2310 5.163953 CCGACCTCAAAATATGCTATTAGCG 60.164 44.000 10.94 0.00 46.26 4.26
1933 2311 5.390991 GCCGACCTCAAAATATGCTATTAGC 60.391 44.000 8.80 8.80 42.82 3.09
1934 2312 5.163953 CGCCGACCTCAAAATATGCTATTAG 60.164 44.000 0.00 0.00 0.00 1.73
1935 2313 4.688879 CGCCGACCTCAAAATATGCTATTA 59.311 41.667 0.00 0.00 0.00 0.98
1936 2314 3.498397 CGCCGACCTCAAAATATGCTATT 59.502 43.478 0.00 0.00 0.00 1.73
1937 2315 3.067106 CGCCGACCTCAAAATATGCTAT 58.933 45.455 0.00 0.00 0.00 2.97
1938 2316 2.479837 CGCCGACCTCAAAATATGCTA 58.520 47.619 0.00 0.00 0.00 3.49
1939 2317 1.299541 CGCCGACCTCAAAATATGCT 58.700 50.000 0.00 0.00 0.00 3.79
1940 2318 0.317020 GCGCCGACCTCAAAATATGC 60.317 55.000 0.00 0.00 0.00 3.14
1941 2319 1.299541 AGCGCCGACCTCAAAATATG 58.700 50.000 2.29 0.00 0.00 1.78
1942 2320 2.902705 TAGCGCCGACCTCAAAATAT 57.097 45.000 2.29 0.00 0.00 1.28
1943 2321 2.902705 ATAGCGCCGACCTCAAAATA 57.097 45.000 2.29 0.00 0.00 1.40
1944 2322 2.038387 AATAGCGCCGACCTCAAAAT 57.962 45.000 2.29 0.00 0.00 1.82
1945 2323 1.816074 AAATAGCGCCGACCTCAAAA 58.184 45.000 2.29 0.00 0.00 2.44
1946 2324 1.466950 CAAAATAGCGCCGACCTCAAA 59.533 47.619 2.29 0.00 0.00 2.69
1947 2325 1.083489 CAAAATAGCGCCGACCTCAA 58.917 50.000 2.29 0.00 0.00 3.02
1948 2326 1.366111 GCAAAATAGCGCCGACCTCA 61.366 55.000 2.29 0.00 0.00 3.86
1949 2327 1.090052 AGCAAAATAGCGCCGACCTC 61.090 55.000 2.29 0.00 40.15 3.85
1950 2328 1.078426 AGCAAAATAGCGCCGACCT 60.078 52.632 2.29 0.00 40.15 3.85
1951 2329 1.062525 CAGCAAAATAGCGCCGACC 59.937 57.895 2.29 0.00 40.15 4.79
1952 2330 1.003851 TACAGCAAAATAGCGCCGAC 58.996 50.000 2.29 0.00 40.15 4.79
1953 2331 1.286501 CTACAGCAAAATAGCGCCGA 58.713 50.000 2.29 0.00 40.15 5.54
1954 2332 0.316196 GCTACAGCAAAATAGCGCCG 60.316 55.000 2.29 0.00 41.59 6.46
1955 2333 3.533913 GCTACAGCAAAATAGCGCC 57.466 52.632 2.29 0.00 41.59 6.53
1958 2336 1.398390 AGCACGCTACAGCAAAATAGC 59.602 47.619 1.61 0.00 42.21 2.97
1959 2337 5.409643 AATAGCACGCTACAGCAAAATAG 57.590 39.130 0.00 0.00 42.21 1.73
1960 2338 5.811399 AAATAGCACGCTACAGCAAAATA 57.189 34.783 0.00 0.00 42.21 1.40
1961 2339 4.701956 AAATAGCACGCTACAGCAAAAT 57.298 36.364 0.00 0.00 42.21 1.82
1962 2340 4.497473 AAAATAGCACGCTACAGCAAAA 57.503 36.364 0.00 0.00 42.21 2.44
1963 2341 4.497473 AAAAATAGCACGCTACAGCAAA 57.503 36.364 0.00 0.00 42.21 3.68
2038 4097 5.129634 TCTTCCATAAATGCCGAATTAGCA 58.870 37.500 5.19 5.19 45.94 3.49
2131 4190 8.103660 TGGGGTCAACTAATAACCATGTAATA 57.896 34.615 0.00 0.00 34.62 0.98
2132 4191 6.975949 TGGGGTCAACTAATAACCATGTAAT 58.024 36.000 0.00 0.00 34.62 1.89
2146 4205 1.077663 AGGATTGCAATGGGGTCAACT 59.922 47.619 18.59 0.00 0.00 3.16
2324 4383 0.104120 GTTTTGCCCCAACGAAGCTT 59.896 50.000 0.00 0.00 0.00 3.74
2334 4393 1.204704 GCTATGTCCAAGTTTTGCCCC 59.795 52.381 0.00 0.00 0.00 5.80
2340 4399 0.679960 GGCGGGCTATGTCCAAGTTT 60.680 55.000 0.00 0.00 0.00 2.66
2348 4407 2.193087 AAAACCTCGGCGGGCTATGT 62.193 55.000 7.21 0.00 36.97 2.29
2690 4755 9.094578 TGGTTTTAAAGACAATTATTGGATGGA 57.905 29.630 9.88 0.00 34.12 3.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.